OK I fixed it.But I'm sure it was caused by FolderSync.
I had to clear the data of "Media storage" and do a full rescan !AFTER! I changed the settings of the folderpairs from the /storage/emulated/legacy (which is the default that FolderSync uses) to /storage/emulated/0 (which is the default that android 4.4.2 uses).
After that the media scanner doesn't scan /storage/emulated/legacy anymore.
Maybe the dev should change the defaults of FolderSync.